PrecisionFDA
Truth Challenge
Engage and improve DNA test results with our community challenges
Explore HG002 comparison results
Use this interactive explorer to filter all results across submission entries and multiple dimensions.
| Entry | Type | Subtype | Subset | Genotype | F-score | Recall | Precision | Frac_NA | Truth TP | Truth FN | Query TP | Query FP | FP gt | % FP ma | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
16101-16150 / 86044 show all | |||||||||||||||
| ckim-gatk | SNP | * | segdup | homalt | 99.4811 | 99.0505 | 99.9155 | 88.5459 | 10641 | 102 | 10641 | 9 | 9 | 100.0000 | |
| cchapple-custom | SNP | tv | map_l150_m0_e0 | het | 94.6151 | 96.4122 | 92.8838 | 85.0097 | 2741 | 102 | 2741 | 210 | 43 | 20.4762 | |
| ckim-dragen | SNP | tv | map_l150_m2_e1 | het | 97.5102 | 98.6119 | 96.4328 | 82.1323 | 7246 | 102 | 7245 | 268 | 17 | 6.3433 | |
| ckim-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 96.4603 | 93.8144 | 99.2597 | 35.4174 | 1547 | 102 | 1743 | 13 | 13 | 100.0000 | |
| ckim-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 99.1021 | 99.2658 | 98.9390 | 69.0925 | 13656 | 101 | 13614 | 146 | 113 | 77.3973 | |
| ckim-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 99.1021 | 99.2658 | 98.9390 | 69.0925 | 13656 | 101 | 13614 | 146 | 113 | 77.3973 | |
| ckim-dragen | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 91.3156 | 84.0190 | 100.0000 | 38.2483 | 531 | 101 | 557 | 0 | 0 | ||
| ciseli-custom | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 53.7560 | 79.3033 | 40.6582 | 61.4881 | 387 | 101 | 383 | 559 | 525 | 93.9177 | |
| cchapple-custom | INDEL | * | map_siren | het | 96.6860 | 97.7595 | 95.6358 | 82.3179 | 4407 | 101 | 4821 | 220 | 56 | 25.4545 | |
| asubramanian-gatk | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 91.8400 | 87.9187 | 96.1276 | 66.5396 | 735 | 101 | 844 | 34 | 30 | 88.2353 | |
| anovak-vg | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 94.8058 | 95.8213 | 93.8116 | 73.3592 | 2316 | 101 | 2380 | 157 | 134 | 85.3503 | |
| astatham-gatk | INDEL | * | map_l125_m2_e0 | het | 94.9267 | 92.7390 | 97.2201 | 89.8845 | 1290 | 101 | 1294 | 37 | 5 | 13.5135 | |
| bgallagher-sentieon | SNP | ti | map_l100_m0_e0 | het | 98.9661 | 99.2777 | 98.6565 | 72.6282 | 13882 | 101 | 13879 | 189 | 28 | 14.8148 | |
| bgallagher-sentieon | SNP | ti | map_l125_m0_e0 | * | 98.9758 | 99.2086 | 98.7441 | 75.3623 | 12661 | 101 | 12659 | 161 | 31 | 19.2547 | |
| jpowers-varprowl | INDEL | * | map_l100_m2_e0 | homalt | 95.3164 | 91.9905 | 98.8917 | 79.6672 | 1160 | 101 | 1160 | 13 | 8 | 61.5385 | |
| ltrigg-rtg1 | INDEL | * | map_l125_m1_e0 | * | 97.1910 | 95.2065 | 99.2600 | 81.6893 | 2006 | 101 | 2012 | 15 | 3 | 20.0000 | |
| jli-custom | SNP | ti | HG002complexvar | homalt | 99.9648 | 99.9478 | 99.9819 | 18.3860 | 193362 | 101 | 193356 | 35 | 26 | 74.2857 | |
| jpowers-varprowl | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 53.1925 | 58.9431 | 48.4642 | 77.5994 | 145 | 101 | 142 | 151 | 149 | 98.6755 | |
| jpowers-varprowl | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 55.1985 | 59.1093 | 51.7730 | 72.4878 | 146 | 101 | 146 | 136 | 136 | 100.0000 | |
| jpowers-varprowl | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 95.1757 | 96.1815 | 94.1907 | 88.8007 | 2544 | 101 | 2578 | 159 | 6 | 3.7736 | |
| rpoplin-dv42 | SNP | * | map_l250_m2_e0 | het | 98.1499 | 98.0554 | 98.2446 | 88.1117 | 5093 | 101 | 5093 | 91 | 56 | 61.5385 | |
| gduggal-bwafb | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 88.8144 | 80.8349 | 98.5418 | 47.2042 | 426 | 101 | 1284 | 19 | 19 | 100.0000 | |
| gduggal-bwafb | SNP | * | lowcmp_SimpleRepeat_quadTR_11to50 | het | 98.1685 | 99.1166 | 97.2384 | 51.9217 | 11332 | 101 | 11373 | 323 | 59 | 18.2663 | |
| dgrover-gatk | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.5315 | 99.4915 | 99.5716 | 59.7014 | 19761 | 101 | 19754 | 85 | 47 | 55.2941 | |
| ckim-isaac | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 93.8949 | 90.4986 | 97.5560 | 73.6447 | 962 | 101 | 958 | 24 | 8 | 33.3333 | |
| ckim-isaac | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 83.9902 | 73.3509 | 98.2394 | 46.3138 | 278 | 101 | 279 | 5 | 4 | 80.0000 | |
| dgrover-gatk | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 97.4696 | 95.8126 | 99.1849 | 62.9471 | 2311 | 101 | 2312 | 19 | 14 | 73.6842 | |
| egarrison-hhga | INDEL | * | map_l100_m1_e0 | * | 97.4160 | 97.1835 | 97.6497 | 97.4833 | 3485 | 101 | 3490 | 84 | 39 | 46.4286 | |
| ckim-vqsr | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.7571 | 99.6017 | 99.9130 | 55.8468 | 25258 | 101 | 25261 | 22 | 14 | 63.6364 | |
| egarrison-hhga | SNP | ti | map_l250_m2_e1 | * | 98.8083 | 98.0102 | 99.6195 | 88.7052 | 4975 | 101 | 4975 | 19 | 9 | 47.3684 | |
| eyeh-varpipe | INDEL | * | map_l100_m2_e0 | het | 96.1330 | 95.6220 | 96.6495 | 82.3053 | 2206 | 101 | 3000 | 104 | 69 | 66.3462 | |
| eyeh-varpipe | INDEL | * | map_siren | homalt | 94.7726 | 96.1959 | 93.3908 | 81.3483 | 2554 | 101 | 2925 | 207 | 162 | 78.2609 | |
| qzeng-custom | INDEL | D6_15 | HG002complexvar | het | 94.9295 | 96.7628 | 93.1643 | 54.7892 | 3019 | 101 | 4116 | 302 | 103 | 34.1060 | |
| mlin-fermikit | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 92.5879 | 91.9586 | 93.2258 | 73.3046 | 1155 | 101 | 1156 | 84 | 55 | 65.4762 | |
| mlin-fermikit | INDEL | D1_5 | map_l125_m2_e0 | homalt | 73.1572 | 72.2527 | 74.0845 | 79.6211 | 263 | 101 | 263 | 92 | 86 | 93.4783 | |
| mlin-fermikit | INDEL | D1_5 | map_l125_m2_e1 | homalt | 73.6413 | 72.8495 | 74.4505 | 79.6193 | 271 | 101 | 271 | 93 | 87 | 93.5484 | |
| mlin-fermikit | INDEL | D1_5 | map_l250_m1_e0 | * | 54.4256 | 40.9357 | 81.1765 | 90.6181 | 70 | 101 | 69 | 16 | 14 | 87.5000 | |
| mlin-fermikit | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 61.7012 | 83.4697 | 48.9383 | 56.4509 | 510 | 101 | 484 | 505 | 504 | 99.8020 | |
| mlin-fermikit | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 90.4777 | 92.0158 | 88.9901 | 86.8129 | 1164 | 101 | 1172 | 145 | 90 | 62.0690 | |
| ltrigg-rtg2 | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 88.2368 | 79.4297 | 99.2405 | 30.2120 | 390 | 101 | 392 | 3 | 3 | 100.0000 | |
| hfeng-pmm1 | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.7867 | 99.6017 | 99.9723 | 54.3769 | 25258 | 101 | 25260 | 7 | 3 | 42.8571 | |
| hfeng-pmm1 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 91.3156 | 84.0190 | 100.0000 | 39.3209 | 531 | 101 | 554 | 0 | 0 | ||
| hfeng-pmm1 | SNP | * | map_l250_m2_e0 | * | 98.8758 | 98.7191 | 99.0331 | 88.4730 | 7784 | 101 | 7784 | 76 | 17 | 22.3684 | |
| hfeng-pmm1 | SNP | tv | map_l125_m1_e0 | het | 99.2869 | 99.0026 | 99.5728 | 70.2971 | 10025 | 101 | 10023 | 43 | 11 | 25.5814 | |
| hfeng-pmm1 | SNP | tv | map_l125_m2_e0 | het | 99.3085 | 99.0328 | 99.5858 | 71.6339 | 10341 | 101 | 10339 | 43 | 11 | 25.5814 | |
| hfeng-pmm1 | SNP | tv | map_l150_m2_e1 | * | 99.3334 | 99.1219 | 99.5459 | 75.2491 | 11401 | 101 | 11399 | 52 | 14 | 26.9231 | |
| hfeng-pmm3 | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.7891 | 99.6426 | 99.9361 | 57.3259 | 28159 | 101 | 28161 | 18 | 11 | 61.1111 | |
| jlack-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 98.0315 | 98.4878 | 97.5794 | 54.7750 | 6578 | 101 | 6571 | 163 | 149 | 91.4110 | |
| hfeng-pmm3 | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 92.9204 | 87.9187 | 98.5255 | 66.5471 | 735 | 101 | 735 | 11 | 9 | 81.8182 | |
| jlack-gatk | SNP | * | map_l250_m1_e0 | het | 90.7389 | 97.8759 | 84.5721 | 93.7676 | 4654 | 101 | 4654 | 849 | 57 | 6.7138 | |